[Go] Spliceform column in GAF

[Chris Mungall]

If a group submitted annotations for two records corresponding to the  
same gene this would be in violation. The most likely way for this to  
happen would be when a MOD submits annotations to both UniProtKB IDs  
and MOD IDs.

On Sep 10, 2008, at 10:34 AM, Stoddard, Alexander wrote:

> I do not clearly understand the following part of the spec regarding
> non-redundant canonical entities:
>
> "In addition the GAF must be non-redundant with respect to canonical
> entities in a genome"
>
> Chris, would you please give an example of how a GAF file could be
> redundant with respect to canonical entities and how to correct the
> example?
>
> Thank you,
> Alex Stoddard
>
>
> -----Original Message-----
> From: go-bounces at genome.stanford.edu
> [mailto:go-bounces at genome.stanford.edu] On Behalf Of Chris Mungall
> Sent: Tuesday, September 09, 2008 5:30 PM
> To: go list; Paul D Thomas
> Subject: [Go] Spliceform column in GAF [was Re: [Gofriends] Redundancy
> ingo_XXXXXX-assocdb-tables/dbxref.txt]
>
> [redirected to GO]
>
> The change Mike speaks of is for the new spliceform column in the GAF.
>
> I have specced this out here:
>
> 	
> http://wiki.geneontology.org/index.php/GAF_Spliceform_Column_Proposal
>
> Note that most of you will have read the previous document describing
> current practices for annotating alternate spliceforms:
>
> 	
> http://wiki.geneontology.org/index.php/Annotation_of_Alternate_Splicefor
> ms
>
> But you won't have read the fully formulated proposal, as I only put
> it on the wiki today.
>
> Note that this proposal was ratified at the SLC GOC meeting, but the
> majority of the discussion was at the RefG portion of the meeting.
> It's particularly important that folks who weren't at this part read
> and understand the proposal. Ratification at the GOC meeting may have
> been premature as I only intended to sketch out a solution
> collaboratively at that meeting.
>
> Once the above wiki page is in shape, we should send an announcement
> to gofriends (promptly, as it is of relevance to the current
> discussion below), all data providers and consumers, and then after
> that in the newsletter and on the main GO docs.
>
> As Mike says we are aiming for a introduction some time in 2009. It's
> important that anyone involved with producing GAFs is aware of the
> changes and is OK with this timetable.
>
> Cheers
> Chris
>
> On Sep 9, 2008, at 1:22 PM, Mike Cherry wrote:
>
>> There is a change coming to the format of the gene association file
>> which will solve this problem.  Annotations to proteins, gene,
>> transcripts, etc for a particular locus will be identified as such.
>> The change should occur in 2009.
>>
>> -Mike
>>
>>
>>> From: "Quaid Morris" <quaid.morris at gmail.com>
>>> To: "Gabriel Berriz" <gberriz at hms.harvard.edu>
>>> Subject: Re: [Gofriends] Redundancy in go_XXXXXX-assocdb-tables/
>>> dbxref.txt
>>> Cc: gofriends at genome.stanford.edu
>>>
>>> Hi Gabriel,
>>>
>>> It looks like in the example that you gave RGD ID 1302948 is a gene
>>> ID and
>>> ENSRNOP00000034933 is a protein ID.  Are all your examples like
>>> this?  Maybe
>>> there are circumstances when it's possible to annotate a specific
>>> isoform
>>> and others when only the gene can be annotated.
>>>
>>> Q
>>>
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>>
>
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